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- EMDB-35268: S-RBD(Omicron BA.3) in complex with PD of ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-35268
TitleS-RBD(Omicron BA.3) in complex with PD of ACE2
Map data
Sample
  • Complex: S-RBD (Omicron BA.3) in complex with PD of ACE2
    • Complex: S-RBD (Omicron BA.3)
      • Protein or peptide: Spike protein S1
    • Complex: PD of ACE2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-Cov-2 / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / viral life cycle / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi YN / Shen YP / Zhang YY / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509301 China
CitationJournal: Viruses / Year: 2023
Title: Structural Basis for the Enhanced Infectivity and Immune Evasion of Omicron Subvariants.
Authors: Yaning Li / Yaping Shen / Yuanyuan Zhang / Renhong Yan /
Abstract: The Omicron variants of SARS-CoV-2 have emerged as the dominant strains worldwide, causing the COVID-19 pandemic. Each Omicron subvariant contains at least 30 mutations on the spike protein (S ...The Omicron variants of SARS-CoV-2 have emerged as the dominant strains worldwide, causing the COVID-19 pandemic. Each Omicron subvariant contains at least 30 mutations on the spike protein (S protein) compared to the original wild-type (WT) strain. Here we report the cryo-EM structures of the trimeric S proteins from the BA.1, BA.2, BA.3, and BA.4/BA.5 subvariants, with BA.4 and BA.5 sharing the same S protein mutations, each in complex with the surface receptor ACE2. All three receptor-binding domains of the S protein from BA.2 and BA.4/BA.5 are "up", while the BA.1 S protein has two "up" and one "down". The BA.3 S protein displays increased heterogeneity, with the majority in the all "up" RBD state. The different conformations preferences of the S protein are consistent with their varied transmissibility. By analyzing the position of the glycan modification on Asn343, which is located at the S309 epitopes, we have uncovered the underlying immune evasion mechanism of the Omicron subvariants. Our findings provide a molecular basis of high infectivity and immune evasion of Omicron subvariants, thereby offering insights into potential therapeutic interventions against SARS-CoV-2 variants.
History
DepositionFeb 6, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35268.png

Downloads & links

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Map

FileDownload / File: emd_35268.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 288 pix.
= 315.36 Å		1.1 Å/pix.
x 288 pix.
= 315.36 Å		1.1 Å/pix.
x 288 pix.
= 315.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.089449264 - 0.10551473
Average (Standard dev.)0.00017346597 (±0.0017911308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 315.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35268_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_35268_half_map_2.map
Projections & Slices
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Sample components

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Entire : S-RBD (Omicron BA.3) in complex with PD of ACE2

EntireName: S-RBD (Omicron BA.3) in complex with PD of ACE2
Components
  • Complex: S-RBD (Omicron BA.3) in complex with PD of ACE2
    • Complex: S-RBD (Omicron BA.3)
      • Protein or peptide: Spike protein S1
    • Complex: PD of ACE2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: S-RBD (Omicron BA.3) in complex with PD of ACE2

SupramoleculeName: S-RBD (Omicron BA.3) in complex with PD of ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: S-RBD (Omicron BA.3)

SupramoleculeName: S-RBD (Omicron BA.3) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: PD of ACE2

SupramoleculeName: PD of ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1

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Macromolecule #1: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.043023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGVKVLFALI CIAVAEAGTS TIEEQAKTFL DKFNHEAEDL FYQSSLASWN YNTNITEENV QNMNNAGDKW SAFLKEQSTL AQMYPLQEI QNLTVKLQLQ ALQQNGSSVL SEDKSKRLNT ILNTMSTIYS TGKVCNPDNP QECLLLEPGL NEIMANSLDY N ERLWAWES ...String:
MGVKVLFALI CIAVAEAGTS TIEEQAKTFL DKFNHEAEDL FYQSSLASWN YNTNITEENV QNMNNAGDKW SAFLKEQSTL AQMYPLQEI QNLTVKLQLQ ALQQNGSSVL SEDKSKRLNT ILNTMSTIYS TGKVCNPDNP QECLLLEPGL NEIMANSLDY N ERLWAWES WRSEVGKQLR PLYEEYVVLK NEMARANHYE DYGDYWRGDY EVNGVDGYDY SRGQLIEDVE HTFEEIKPLY EH LHAYVRA KLMNAYPSYI SPIGCLPAHL LGDMWGRFWT NLYSLTVPFG QKPNIDVTDA MVDQAWDAQR IFKEAEKFFV SVG LPNMTQ GFWENSMLTD PGNVQKAVCH PTAWDLGKGD FRILMCTKVT MDDFLTAHHE MGHIQYDMAY AAQPFLLRNG ANEG FHEAV GEIMSLSAAT PKHLKSIGLL SPDFQEDNET EINFLLKQAL TIVGTLPFTY MLEKWRWMVF KGEIPKDQWM KKWWE MKRE IVGVVEPVPH DETYCDPASL FHVSNDYSFI RYYTRTLYQF QFQEALCQAA KHEGPLHKCD ISNSTEAGQK LFNMLR LGK SEPWTLALEN VVGAKNMNVR PLLNYFEPLF TWLKDQNKNS FVGWSTDWSP YAD

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Details: Omicron BA.3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 25.418885 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNFAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGNEV RQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKVSG NYNYLYRLFR KSNLKPFERD ISTEIYQAGN K PCNGVAGF ...String:
RVQPTESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNFAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGNEV RQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKVSG NYNYLYRLFR KSNLKPFERD ISTEIYQAGN K PCNGVAGF NCYFPLRSYG FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNF

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 884258
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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